INSTRUCTIONS TO AUTHORS - aem.asm.org

1 October 2019, INSTRUCTIONS to AUTHORS , pages 1 21. INSTRUCTIONS TO AUTHORS . SCOPE cesses and evolutionary relationships among microorganisms. Topics include genomic analysis of microorganisms and met- Applied and Environmental Microbiology (AEM) publishes agenomic investigation of microbiomes in the environment. descriptions of all aspects of applied microbial research, basic (Meta)genome analyses that do not provide significant new research on microbial ecology, and research of a genetic and insights into the microbiology of the system(s) under study molecular nature that focuses on microbial topics of practical will normally not be acceptable for publication in AEM. value. Research must address salient microbiological princi- The food microbiology section covers manuscripts dealing ples, fundamental microbial processes, or basic questions in with all aspects of food microbiology, including microbial food applied or environmental microbiology.

2 Topics that are con- pathogens, microbial ecology of foods, predictive food micro- sidered include microbiology in relation to foods, agriculture, biology, food fermentations, food spoilage, probiotics, and industry, biotechnology, public health, plants, and inverte- prebiotics. Manuscripts reporting on the effects of probiotics or brates and basic biological properties of bacteria, fungi, algae, prebiotics should provide new insights into the mechanism(s). protozoa, and other simple eukaryotic organisms as related to Manuscripts detailing the occurrence of microbial toxins or mi- microbial ecology. Manuscripts should report new and signif- crobial metabolites are suitable if the work includes significant icant findings that advance the understanding of microbiology information on the microbe and its toxin or metabolite produc- and upon which other scientists may build.

3 To best serve its tion. This section also includes studies on the gastrointestinal tract readership, the journal must accept only those papers that are microbiome as it relates to molecular toxicology, diet, and nutri- most significant to the field of applied and environmental mi- tion. Molecular assessments of food microbiomes should follow crobiology. Thus, the editors will reject manuscripts that, while guidelines for the microbial ecology section. scientifically sound, represent only incremental extensions of The genetics and molecular biology section includes papers other studies, are mainly confirmatory, or do not pursue a describing genetic organization, expression, mutation, and re- question in sufficient depth. pair in organisms with environmental or practical significance. AEM publishes minireviews that provide forward-reaching Manuscripts for the geomicrobiology section must empha- assessments of topics of current relevance to the diverse sec- size the role of microorganisms in geobiochemical processes in tions of the journal.

4 Additional information on minireviews terrestrial or aquatic ecosystems, including subsurface, aquifer, can be found in a subsequent part of these INSTRUCTIONS . and oceanic environments. Topics include mineralization, the AEM welcomes microbiome studies that address the micro- use of inorganic ions in energy metabolism, and growth in biology and functions of natural or experimental systems. The extreme environments. Manuscripts focused on geological nature of the microbiome study will determine in which sec- processes with only marginal links to microbiology will not tion of the journal it will be published. qualify for AEM. The biodegradation section describes novel microbial pro- Invertebrate microbiology manuscripts should address in- cesses for alteration, removal, or utilization of environmental teractions between invertebrates and microorganisms, ranging or anthropogenic chemicals.

5 From commensalism and mutualism to parasitism and pathoge- Papers in the biotechnology section describe the use and nicity. Manuscripts describing work dealing with the metabolites modification of organisms in order to achieve socially benefi- or toxins from animal, plant, or insect cells or the physiology of cial objectives. such cells are not suitable for AEM unless the work concerns a The environmental microbiology section covers manu- microbial community or individual microorganisms. scripts that focus on research related to microorganisms in the New microbiological methods must provide novel avenues environment. This is distinct from the microbial ecology sec- to address fundamental biological questions and will be con- tion, which focuses on ecological relationships, such as inter- sidered for publication in AEM when accompanied by a actions among organisms, their structure and functional role demonstrated application.

6 Descriptions of the application in an ecosystem, and community-level studies. Thus, the envi- of previously described technologies, including the cloning, ronmental microbiology section features articles that focus on amplification, and expression of foreign genes, to a new genus specific organisms in the environment, rather than a whole or species of microbe will generally not be considered for indepen- community, as well as those in which the study is not focused dent publication. Manuscripts that describe the construction of on implied or stated underlying ecological relationships. engineered strains for innovative process application, develop- The enzymology and protein engineering section covers a ment, or enhancement must present results to authenticate the broad range of topics relative to microbial catalysis and in- utility, superiority, and uniqueness of such strains.

7 Cludes papers describing (i) the structure and function of en- The microbial ecology section covers a wide range of topics on vironmentally or industrially significant proteins and how they the ecology of microorganisms, including culture-independent can be modified to achieve practical catalytic objectives and (ii). the enzymology or biosynthesis of fungal, algal, and bacterial metabolites or toxins of importance to the environment or to Copyright 2019 American Society for Microbiology. All Rights Reserved. society. INSTRUCTIONS to AUTHORS are updated throughout the year. The current version is Included in the evolutionary and genomic microbiology available on the journal website. section are papers detailing newly described evolutionary pro- October 2019, INSTRUCTIONS to AUTHORS Applied and Environmental Microbiology 1.

8 INSTRUCTIONS to AUTHORS molecular assessments that provide new insights into (i) the antimicrobial agents, including manuscripts dealing with the structure-function relationships of microorganisms, (ii) the biosynthesis and metabolism of such agents, are more appro- impact of in situ conditions on community structure, or (iii) priate for Antimicrobial Agents and Chemotherapy . the effect of changes in microbial community composition on (iii) AEM will consider manuscripts that concern bacte- ecosystem function. Phylogenetic assessments that do not pro- riophages or other viruses in relation to the environment, vide such insights will normally not be acceptable for publica- public health, or industrial microbiology. Papers that pri- tion in AEM. marily concern attachment and intracellular replication of The physiology section addresses questions about how or- viruses, virus interactions with host metabolism, virus ganisms adapt to changes in their environment, including bio- structure, or virus genomics are more appropriate for the energetics, stress, starvation, metabolic challenges, and re- Journal of Virology.

9 Sponses to nutritional variation. (iv) Manuscripts dealing with the immune system or with The plant microbiology section covers manuscripts dealing topics of basic medical interest or oral microbiology are more with all aspects of plant-microorganism interactions, includ- appropriate for Infection and Immunity . Reports of clinical ing symbiotic and rhizosphere bacteria as well as phytopatho- investigations and environmental biology applied to hospitals genic microorganisms. should be submitted to the Journal of Clinical Microbiology . The public and environmental health microbiology sec- (v) AEM and mSphere accept manuscripts on population tion is focused primarily on environmentally transmitted mi- dynamics and the ecology of eukaryotic microbes. Studies of croorganisms that affect human health. Environmental health microbial communities and of microbial populations with microbiology is a branch of public health concerned with the identified economic or ecological significance, , plant environmental occurrence of disease-causing microbes and pathogens or symbionts, are usually more appropriate with creating health-supportive environments.

10 Microbes of a for AEM. zoonotic nature or microbes transmitted through water, soil, (vi) Manuscripts dealing with the purification and charac- or environmental surfaces are of special interest. terization of enzymes or cloning of genes that have already AEM is not specialized in the systematics of prokaryotes, been extensively described for other organisms will be consid- but taxonomic papers that describe a new prokaryotic taxon ered for publication only if they offer experimentally sup- are welcome when phylogenetic or genotypic data are ac- ported new insights into the biological role, properties, or ap- companied by a significant amount of information that goes plications of these enzymes. Descriptions of genes or enzymes beyond the taxonomic description of the new taxon. Such that differ only in minor ways from the prototypes are not additional information might include information on the suitable for AEM.